Say for example, if the nature selects a clone of bacteria to be resistant to a specific antibiotic, what actually happens to the bacterial genotype and physiology that brings about resistance? What is the basis of selection of a specific clone?
The genotype of a clone that is resistant to a specific antibiotic changes in support to the resistance mechanism needed for the clone to be resistant to the antibiotic in the first place.
The following article may help you in your second question: Article The determinants of the antibiotic resistance process
I may add to Anzaldo s answer that the natural selection consists in the survival if the most fit genotype bacteria. This means that the one who acquired resistance will survive to the action of the antibiotic while the non resistant bacteria are eliminated by the antibiotic. The final result is that the resistant bacteria will thrive and grow and fully replace the non resistant ones.
physiology that brings about resistance = one of those mechanisms, destroying the antibiotic in the extracellular medium (hydrolytic enzyme), blocking its entry in the cell at the level of the membrane (modified permease), diluting the antibiotic in the cytoplasm (modified pathway or target mimetics), modifying its target through mutation (loss of the antibiotic fixation site)
the basis of selection of a specific clone = other clones are killed or considerably disadvantaged in the competition for niche and food!
Changes in ‘phenotypic landscape’ of a population within a generation can be produced by three independent processes: migration, development and selection.
Natural selection is a process, not a mechanism. What are the mechanisms, or causal agents, of this process? The agents of selection must be investigated between environmental variables (e.g., partners, resources, enemies, hazards) that provide the assotiation between fitness (viability and fecundity) and phenotype. Remembering that not every agent of selection is a source of mortality, as well as not all sources of mortality are agents of selection.
Natural selection is essentially an ecological process and, in this sense, I think it would be worth consulting:
+ Roughgarden. 1979. Theory of population genetics and evolutionary ecology: An introduction. NY, Macmillan;
+ Vermeij. 1987. Evolution and escalation: An ecological history of life. Princeton, PUP;
+ Wade & Kalisz. 1990. The causes of natural selection. Evolution 44: 1947-55; and
+ MacColl. 2011. The ecological causes of evolution. Trends in Ecology and Evolution 26: 514-22.
Darwin described one route of evolution (slow evolution within a same species) and only mentioned and discharged the 2nd route (direct jump from one species to a new one). The currently accepted mechanism , 1st route, is not dominant. The prove that it is not dominant is that it demands finding the so called "lost links" and, til now, not even one single lost link has ever been found. This is a strong evidence that the dominant way (maybe the only way) is the 2nd route but researchers keep trying to find the lost links.